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Estimated time of infection vs. confirmed infections

Following the ideas from Tomas Pueyo's Medium post "Coronavirus: Why You Must Act Now" [1], we assume the average time from infection to death at 23 days [2]. The data is pulled from the COVID-19 Data Repository by Johns Hopkins CSSE [3] every hour. Countries with a minimnum of 1000 confirmed cases and 40 confirmed deaths are included in this analysis.

The time from infection to death is equal to the incubation period plus the time from symptoms to death. This is used to estimate the time of the infections that lead to the observed deaths. We take the last fatality rate per country (total_cases/total_deaths) to estimate the number of infections that are responsible for the observed deaths.

In the figures below, you can observe successive waves of infections (dashed), detections (black) and deaths (red) for each country. The upper panel shows the absolute number of events. The dashed lines show the estimated number of infections. The lower panel shows the normalized number of events. Here the temporal delay between the waves and the relative change between each other can be observed.

[1] https://medium.com/@tomaspueyo/coronavirus-act-today-or-people-will-die-f4d3d9cd99ca

[2] https://github.com/midas-network/COVID-19/tree/master/parameter_estimates/2019_novel_coronavirus

[3] https://github.com/CSSEGISandData/COVID-19/tree/master/csse_covid_19_data/csse_covid_19_time_series

US
Brazil
Mexico
United Kingdom
India
Italy
France
Spain
Peru
Iran
Russia
Colombia
Belgium
Chile
Germany
Canada
South Africa
Netherlands
Pakistan
Ecuador
Turkey
Sweden
Indonesia
Iraq
Egypt
China
Argentina
Bolivia
Bangladesh
Saudi Arabia
Romania
Philippines
Guatemala
Switzerland
Ireland
Ukraine
Portugal
Poland
Panama
Kyrgyzstan
Honduras
Afghanistan
Algeria
Dominican Republic
Japan
Nigeria
Moldova
Kazakhstan
Armenia
Sudan
Austria
Denmark
Serbia
Belarus
Israel
North Macedonia
El Salvador
Azerbaijan
Kuwait
Oman
Bulgaria
Morocco
Cameroon
Czechia
Kenya
Bosnia and Herzegovina
United Arab Emirates
Ethiopia
South Korea
Australia
Senegal
Ghana
Venezuela
Qatar
Costa Rica
Uzbekistan
Bahrain
Madagascar
Cote d'Ivoire

Ahead of the curve

Some countries start testing the population earlier in the outbreak than others. The time delay between the wave of deaths and the wave of confirmed cases is indicative for how early a country is detecting new cases ahead of the increase of deaths. Earlier detection means a better chances for successful isolation of an infected person and treatment of the desease.

We measure the distance of the maximum of cumulative deaths and new deaths to the number of infections to estimate the progression of the infection across countries.

If, in the early phase of the infection wave, the number of deaths rises faster than the number of confirmed cases, the distance drops, indicating that

A comparison of countries with respect to their mean time for reponse is presented below.

To determine the above values, we plot the number of confirmed cases (solid black lines) and the number of deaths (dashed black lines). From this, we measure the distance of the day of maximum deaths (dashed red lines) to the day of confirmed cases at this y-value.

The distance is indicative for how fast the humber of confirmed cases increases comapred to the increase of the number of deaths.

US
Brazil
Mexico
United Kingdom
India
Italy
France
Spain
Peru
Iran
Russia
Colombia
Belgium
Chile
Germany
Canada
South Africa
Netherlands
Pakistan
Ecuador
Turkey
Sweden
Indonesia
Iraq
Egypt
China
Argentina
Bolivia
Bangladesh
Saudi Arabia
Romania
Philippines
Guatemala
Switzerland
Ireland
Ukraine
Portugal
Poland
Panama
Kyrgyzstan
Honduras
Afghanistan
Algeria
Dominican Republic
Japan
Nigeria
Moldova
Kazakhstan
Armenia
Sudan
Austria
Denmark
Serbia
Belarus
Israel
North Macedonia
El Salvador
Azerbaijan
Kuwait
Oman
Bulgaria
Morocco
Cameroon
Czechia
Kenya
Bosnia and Herzegovina
United Arab Emirates
Ethiopia
South Korea
Australia
Senegal
Ghana
Venezuela
Qatar
Costa Rica
Uzbekistan
Bahrain
Madagascar
Cote d'Ivoire